Neoantigen prediction and HLA binding
From your somatic variants and the patient’s HLA alleles: peptide–HLA binding prediction and prioritization of candidate neoantigens with an open-source predictor (no reliance on proprietary licenses).
From mutation to candidate
We turn the tumor’s variants into mutant peptides, predict their binding to the patient’s HLA alleles and rank them by immunogenic potential.
Mutant peptides
Translation of variants (missense and in-frame indels) into peptides of the appropriate length for MHC class I.
8–11 aaPeptide–HLA binding
Affinity (IC50) and percentile prediction with MHCflurry (class I); classification into binder and strong binder.
IC50 · %rankHLA typing
We start from the patient’s HLA typing (from sequencing or the one you provide) to restrict the prediction to their alleles.
A/B/CPrioritization
Ranking by agretopicity (better binding of the mutant than the wild-type) to highlight the most tumor-specific candidates.
log₂(wt/mt)pVACseq workflow
Complete workflow from the annotated VCF (VEP) + HLA to the table of filtered epitopes, with the predictor configured.
VEP + pVACseqResults
Table of prioritized epitopes with gene, mutation, peptide, allele, IC50 and percentile; summary of the top candidates.
TSV + reportFour steps
1. Data
Annotated somatic VCF (VEP) + patient’s HLA alleles.
2. Peptides
Generation of mutant and wild-type peptides.
3. Prediction
MHCflurry for each peptide × patient allele.
4. Prioritization
Ranking by agretopicity and candidate report.
What it includes
Generation of mutant peptides, binding prediction to the patient’s HLA alleles, binder/strong classification, prioritization by agretopicity and report. Volume and academic discounts.
Honest limits
The prediction covers MHC class I with an open-source predictor. A good binder does not imply immunogenicity: the ranking prioritizes candidates that experimental validation (e.g. multimers, ELISpot) must confirm. Class II is out of scope due to licensing. We deliver everything as research (RUO).
Shall we prioritize your neoantigens?
Send us the annotated somatic VCF and the HLA typing; we get back to you with a quote and timeline within 48 h.